Rev Language Reference



dnCTMC(RateGenerator Q, Simplex rootFrequencies, Simplex siteMatrices, RealPos[] siteRates, Simplex siteRatesProbs, Natural nSites, String type)


Q : RateGenerator (pass by const reference)
The global or site-mixture rate matrices.
rootFrequencies : Simplex (pass by const reference)
The root specific frequencies of the characters, if applicable.
Default : NULL
siteMatrices : Simplex (pass by const reference)
Simplex of site matrix mixture probabilities. Treats Q as vector of site mixture categories instead of branch-specific matrices.
Default : NULL
siteRates : RealPos[] (pass by const reference)
The rate categories for the sites.
Default : [ ]
siteRatesProbs : Simplex (pass by const reference)
The probability weights of rate categories for the sites.
Default : NULL
nSites : Natural (pass by value)
The number of sites, used for simulation.
Default : 0
type : String (pass by value)
The data type, used for simulation and initialization.
Default : DNA
Options : DNA|RNA|AA|Codon|PoMo|Protein|Standard|NaturalNumbers|Binary|Restriction

Domain Type